We have shown that electron energy loss spectroscopic imaging (EELS) in the scanning transmission electron microscope (STEM) can provide single atom sensitivity for elements such as calcium and iron bound to proteins adsorbed onto thin carbon films. A spectrum-imaging system incorporating a 100x1340 pixel CCD detector enables collection of parallel EELS data at each image pixel. Advantages of this new system are (i) the low noise level that provides higher analytical sensitivity, (ii) the short read-out time of around 10 ms, which provides faster acquisition, (iii) the two-dimensional array of square pixels, which allows exact correction for channel gain variations, and (iv) the improved point-spread function of the optical coupling of the detector array to the scintillator. Compensation for specimen drift is achieved in real-time by cross-correlating annular dark-field images recorded at the end of each scan line. Using ferritin molecules as a reference structure, iron maps have been obtained from individual hemoglobin molecules showing detection of four iron atoms per molecule. By absorbing a very low salt concentration onto a carbon support film, it is feasible to image single atoms of calcium using this system. Possible future applications include the characterization of individual macromolecules that contain bound atoms of specific elements.